PhyloGraphUtil

A tool to compare and convert between different network formats.

Features

• Compare between 2 networks using
  • Robinson Foulds
  • Jaccard index
  • F1 Score
• Convert one format into another
  • Note: Most information about the network for certain things/attributes will be lost, such as internal node names, length, weights, etc.
  • While the graph may be the same in terms of structure, the output may look different, as in, GML -> Extended Newick -> GML may or may not produce something that looks different.

Formats

• ✔ - Supported
• ❌ - Not supported
• 📎 - Planned

Formats	Extension(s)	Open	Save
GML	.gml	✔	✔
Extended Newick	.enwk, .ewk	✔	✔
Admixtools admixture	.admix	✔	✔
Simple admixture	.sadmix	📎	📎
Treemix	.treemix	✔	❌

Usage/Examples

PhyloGraphUtil

USAGE:
        PhyloGraphUtil <SUBCOMMAND>

FLAGS:
        -h      Prints help information for this and each subcommand.

SUBCOMMANDS:
        convert Converts from one graph format to another.
        compare Compares one graph to another using a specified method.
        print   Prints basic info of the read-in graph(s).

FORMATS:
        GML     .gml
        ENWK    .enwk, .ewk
        ADMIX   .admix
        TREEMIX .treemix

Converting GML to Extended Newick:

PhyloGraphUtil convert test.gml ENWK

Comparing 2 different networks using Robinson Foulds:

PhyloGraphUtil compare rf A.gml B.enwk

Build

Simply run make, and the executable will be found in the bin folder.

Roadmap

• More formats
• Different methods for conversion
• Better way to open and parse the different formats
  • Maybe supporting different file extensions for the same format, for example, enwk or ewk for Extended Newick
• When converting to certain formats, be able to customize the output, such as including internal names and whatnot

Credit

• Jonker-Volgenant's algorithm for Linear Assignment Problem